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Xu K, Ji S, Huang J, Yin L, Zhang J, Sun R, Pu Y. ZMAT3 participated in benzene-caused disruption in self-renewal and differentiation of hematopoietic stem cells via TNF-α/NF-κB pathway. Food Chem Toxicol 2024; 190:114838. [PMID: 38914192 DOI: 10.1016/j.fct.2024.114838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 06/05/2024] [Accepted: 06/21/2024] [Indexed: 06/26/2024]
Abstract
Benzene is a common environmental and occupational pollutant, benzene exposure causes damage to hematopoietic system. ZMAT3 is a zinc finger protein which has important biological functions. In this study, benzene-exposed mouse model and ZMAT3 overexpression and low expression hematopoietic stem cells (HSCs) models were constructed to explore the mechanism of ZMAT3 in benzene-induced hematopoietic toxicity. The results showed that benzene increased the expression of ZMAT3 in mouse bone marrow (BM) cells, HSCs and peripheral blood (PB) leukocyte, and the changes in HSCs were more sensitive than BM and PB cells. In addition, overexpression of ZMAT3 decreased the self-renewal ability of HSCs and reduced the HSCs differentiation into myeloid hematopoietic cells, while low expression has the opposite effect. Besides, over and low expression of ZMAT3 both increased the HSCs differentiation into lymphoid progenitor cells. Moreover, bioinformatics analysis suggested that ZMAT3 was associated with TNF-α signaling pathway, and the correlation was confirmed in mouse model. Meanwhile, the results indicated that ZMAT3 promoted TNF-α mRNA processing by binding to the ARE structural domain on TNF-α and interacting with hnRNP A2/B1 and hnRNP A1 proteins, ultimately activating the NF-κB signaling pathway. This study provides a new mechanism for the study of benzene toxicity.
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Affiliation(s)
- Kai Xu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China
| | - Shuangbin Ji
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China
| | - Jiawei Huang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China
| | - Lihong Yin
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China
| | - Juan Zhang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China
| | - Rongli Sun
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China.
| | - Yuepu Pu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, China.
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2
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Groven RVM, Kuik C, Greven J, Mert Ü, Bouwman FG, Poeze M, Blokhuis TJ, Huber-Lang M, Hildebrand F, Cillero-Pastor B, van Griensven M. Fracture haematoma proteomics. Bone Joint Res 2024; 13:214-225. [PMID: 38699779 PMCID: PMC11090216 DOI: 10.1302/2046-3758.135.bjr-2023-0323.r1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/05/2024] Open
Abstract
Aims The aim of this study was to determine the fracture haematoma (fxH) proteome after multiple trauma using label-free proteomics, comparing two different fracture treatment strategies. Methods A porcine multiple trauma model was used in which two fracture treatment strategies were compared: early total care (ETC) and damage control orthopaedics (DCO). fxH was harvested and analyzed using liquid chromatography-tandem mass spectrometry. Per group, discriminating proteins were identified and protein interaction analyses were performed to further elucidate key biomolecular pathways in the early fracture healing phase. Results The early fxH proteome was characterized by immunomodulatory and osteogenic proteins, and proteins involved in the coagulation cascade. Treatment-specific proteome alterations were observed. The fxH proteome of the ETC group showed increased expression of pro-inflammatory proteins related to, among others, activation of the complement system, neutrophil functioning, and macrophage activation, while showing decreased expression of proteins related to osteogenesis and tissue remodelling. Conversely, the fxH proteome of the DCO group contained various upregulated or exclusively detected proteins related to tissue regeneration and remodelling, and proteins related to anti-inflammatory and osteogenic processes. Conclusion The early fxH proteome of the ETC group was characterized by the expression of immunomodulatory, mainly pro-inflammatory, proteins, whereas the early fxH proteome of the DCO group was more regenerative and osteogenic in nature. These findings match clinical observations, in which enhanced surgical trauma after multiple trauma causes dysbalanced inflammation, potentially leading to reduced tissue regeneration, and gained insights into regulatory mechanisms of fracture healing after severe trauma.
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Affiliation(s)
- Rald V. M. Groven
- Department of Cell Biology-Inspired Tissue Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, Maastricht, Netherlands
- Division of Trauma Surgery, Department of Surgery, Maastricht University Medical Center+, Maastricht, Netherlands
| | - Christel Kuik
- Maastricht Multimodal Molecular Imaging (M4i) Institute, Division of Imaging Mass Spectrometry, Maastricht University, Maastricht, Netherlands
| | - Johannes Greven
- Experimental Orthopaedics and Trauma Surgery, Department of Orthopaedics, Trauma and Reconstructive Surgery, University Hospital RWTH Aachen, Aachen, Germany
| | - Ümit Mert
- Department of Orthopaedics, Trauma and Reconstructive Surgery, University Hospital RWTH Aachen, Aachen, Germany
| | - Freek G. Bouwman
- NUTRIM, School for Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, Netherlands
| | - Martijn Poeze
- Division of Trauma Surgery, Department of Surgery, Maastricht University Medical Center+, Maastricht, Netherlands
| | - Taco J. Blokhuis
- Division of Trauma Surgery, Department of Surgery, Maastricht University Medical Center+, Maastricht, Netherlands
| | - Markus Huber-Lang
- Institute of Clinical and Experimental Trauma Immunology, University Hospital Ulm, Ulm, Germany
| | - Frank Hildebrand
- Department of Orthopaedics, Trauma and Reconstructive Surgery, University Hospital RWTH Aachen, Aachen, Germany
| | - Berta Cillero-Pastor
- Department of Cell Biology-Inspired Tissue Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, Maastricht, Netherlands
- Maastricht Multimodal Molecular Imaging (M4i) Institute, Division of Imaging Mass Spectrometry, Maastricht University, Maastricht, Netherlands
| | - Martijn van Griensven
- Department of Cell Biology-Inspired Tissue Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, Maastricht, Netherlands
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Christie J, Anthony CM, Harish M, Mudartha D, Ud Din Farooqee SB, Venkatraman P. The interaction network of the proteasome assembly chaperone PSMD9 regulates proteostasis. FEBS J 2023; 290:5581-5604. [PMID: 37665644 DOI: 10.1111/febs.16948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 08/09/2023] [Accepted: 09/01/2023] [Indexed: 09/06/2023]
Abstract
Functional networks in cells are created by physical, genetic, and regulatory interactions. Mapping them and annotating their functions by available methods remains a challenge. We use affinity purification mass spectrometry (AP-MS) coupled with SLiMFinder to discern such a network involving 26S proteasome non-ATPase regulatory subunit 9 (PSMD9), a chaperone of proteasome assembly. Approximately 20% of proteins within the PSMD9 interactome carry a short linear motif (SLiM) of the type 'EXKK'. The binding of purified PSMD9 with the peptide sequence ERKK, proteins heterogeneous nuclear ribonucleoproteins A2/B1 (hnRNPA2B1; containing ERKK), and peroxiredoxin-6 (PRDX6; containing EAKK) provided proof of principle for this motif-driven network. The EXKK motif in the peptide primarily interacts with the coiled-coil N domain of PSMD9, a unique interaction not reported for any coiled-coil domain. PSMD9 knockout (KO) HEK293 cells experience endoplasmic reticulum (ER) stress and respond by increasing the unfolded protein response (UPR) and reducing the formation of aggresomes and lipid droplets. Trans-expression of PSMD9 in the KO cells rescues lipid droplet formation. Overexpression of PSMD9 in HEK293 cells results in reduced UPR, and increased lipid droplet and aggresome formation. The outcome argues for the prominent role of PSMD9 in maintaining proteostasis. Probable mechanisms involve the binding of PSMD9 to binding immunoglobulin protein (BIP/GRP78; containing EDKK), an endoplasmic reticulum chaperone and key regulator of the UPR, and fatty acid synthase (FASN; containing ELKK), involved in fatty acid synthesis/lipid biogenesis. We propose that PSMD9 acts as a buffer in the cellular milieu by moderating the UPR and enhancing aggresome formation to reduce stress-induced proteotoxicity. Akin to waves created in ponds that perpetuate to a distance, perturbing the levels of PSMD9 would cause ripples down the networks, affecting final reactions in the pathway, one of which is altered proteostasis.
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Affiliation(s)
- Joel Christie
- Protein Interactome Lab for Structural and Functional Biology, Advanced Centre for Treatment Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - C Merlyn Anthony
- Protein Interactome Lab for Structural and Functional Biology, Advanced Centre for Treatment Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Mahalakshmi Harish
- Protein Interactome Lab for Structural and Functional Biology, Advanced Centre for Treatment Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Deepti Mudartha
- Protein Interactome Lab for Structural and Functional Biology, Advanced Centre for Treatment Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India
| | - Sheikh Burhan Ud Din Farooqee
- Protein Interactome Lab for Structural and Functional Biology, Advanced Centre for Treatment Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India
| | - Prasanna Venkatraman
- Protein Interactome Lab for Structural and Functional Biology, Advanced Centre for Treatment Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
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Tychhon B, Allen JC, Gonzalez MA, Olivas IM, Solecki JP, Keivan M, Velazquez VV, McCall EB, Tapia DN, Rubio AJ, Jordan C, Elliott D, Eiring AM. The prognostic value of 19S ATPase proteasome subunits in acute myeloid leukemia and other forms of cancer. Front Med (Lausanne) 2023; 10:1209425. [PMID: 37502358 PMCID: PMC10371016 DOI: 10.3389/fmed.2023.1209425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 06/05/2023] [Indexed: 07/29/2023] Open
Abstract
Introduction The ubiquitin-proteasome system (UPS) is an intracellular organelle responsible for targeted protein degradation, which represents a standard therapeutic target for many different human malignancies. Bortezomib, a reversible inhibitor of chymotrypsin-like proteasome activity, was first approved by the FDA in 2003 to treat multiple myeloma and is now used to treat a number of different cancers, including relapsed mantle cell lymphoma, diffuse large B-cell lymphoma, colorectal cancer, and thyroid carcinoma. Despite the success, bortezomib and other proteasome inhibitors are subject to severe side effects, and ultimately, drug resistance. We recently reported an oncogenic role for non-ATPase members of the 19S proteasome in chronic myeloid leukemia (CML), acute myeloid leukemia (AML), and several different solid tumors. In the present study, we hypothesized that ATPase members of the 19S proteasome would also serve as biomarkers and putative therapeutic targets in AML and multiple other cancers. Methods We used data from The Cancer Genome Atlas (TCGA) and the Clinical Proteomic Tumor Analysis Consortium (CPTAC) available at UALCAN and/or GEPIA2 to assess the expression and prognostic value of proteasome 26S subunit, ATPases 1-6 (PSMC1-6) of the 19S proteasome in cancer. UALCAN was also used to associate PSMC1-6 mRNA expression with distinct clinicopathological features. Finally, cBioPortal was employed to assess genomic alterations of PSMC genes across different cancer types. Results The mRNA and protein expression of PSMC1-6 of the 19S proteasome were elevated in several cancers compared with normal controls, which often correlated with worse overall survival. In contrast, AML patients demonstrated reduced expression of these proteasome subunits compared with normal mononuclear cells. However, AML patients with high expression of PSMC2-5 had worse outcomes. Discussion Altogether, our data suggest that components of the 19S proteasome could serve as prognostic biomarkers and novel therapeutic targets in AML and several other human malignancies.
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Affiliation(s)
- Boranai Tychhon
- Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center at El Paso, El Paso, TX, United States
| | - Jesse C. Allen
- Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center at El Paso, El Paso, TX, United States
| | - Mayra A. Gonzalez
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Texas Tech University Health Sciences Center at El Paso, El Paso, TX, United States
| | - Idaly M. Olivas
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Texas Tech University Health Sciences Center at El Paso, El Paso, TX, United States
| | - Jonathan P. Solecki
- L. Frederick Francis Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center at El Paso, El Paso, TX, United States
| | - Mehrshad Keivan
- L. Frederick Francis Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center at El Paso, El Paso, TX, United States
| | - Vanessa V. Velazquez
- Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center at El Paso, El Paso, TX, United States
| | - Emily B. McCall
- Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center at El Paso, El Paso, TX, United States
| | - Desiree N. Tapia
- Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center at El Paso, El Paso, TX, United States
| | - Andres J. Rubio
- Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center at El Paso, El Paso, TX, United States
| | - Connor Jordan
- L. Frederick Francis Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center at El Paso, El Paso, TX, United States
| | - David Elliott
- Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center at El Paso, El Paso, TX, United States
| | - Anna M. Eiring
- Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center at El Paso, El Paso, TX, United States
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Texas Tech University Health Sciences Center at El Paso, El Paso, TX, United States
- L. Frederick Francis Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center at El Paso, El Paso, TX, United States
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Suzuki M, Kuromi H, Shindo M, Sakata N, Niimi N, Fukui K, Saitoe M, Sango K. A Drosophila model of diabetic neuropathy reveals a role of proteasome activity in the glia. iScience 2023; 26:106997. [PMID: 37378316 PMCID: PMC10291573 DOI: 10.1016/j.isci.2023.106997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 03/31/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
Diabetic peripheral neuropathy (DPN) is the most common chronic, progressive complication of diabetes mellitus. The main symptom is sensory loss; the molecular mechanisms are not fully understood. We found that Drosophila fed a high-sugar diet, which induces diabetes-like phenotypes, exhibit impairment of noxious heat avoidance. The impairment of heat avoidance was associated with shrinkage of the leg neurons expressing the Drosophila transient receptor potential channel Painless. Using a candidate genetic screening approach, we identified proteasome modulator 9 as one of the modulators of impairment of heat avoidance. We further showed that proteasome inhibition in the glia reversed the impairment of noxious heat avoidance, and heat-shock proteins and endolysosomal trafficking in the glia mediated the effect of proteasome inhibition. Our results establish Drosophila as a useful system for exploring molecular mechanisms of diet-induced peripheral neuropathy and propose that the glial proteasome is one of the candidate therapeutic targets for DPN.
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Affiliation(s)
- Mari Suzuki
- Diabetic Neuropathy Project, Tokyo Metropolitan Institute of Medical Science, Setagaya, Tokyo 156-8506, Japan
| | - Hiroshi Kuromi
- Learning and Memory Project, Tokyo Metropolitan Institute of Medical Science, Setagaya, Tokyo 156-8506, Japan
| | - Mayumi Shindo
- Center for Basic Technology Research, Tokyo Metropolitan Institute of Medical Science, Setagaya, Tokyo 156-8506, Japan
| | - Nozomi Sakata
- Diabetic Neuropathy Project, Tokyo Metropolitan Institute of Medical Science, Setagaya, Tokyo 156-8506, Japan
- Department of Bioscience and Engineering, Shibaura Institute of Technology, Saitama 337-8570, Japan
| | - Naoko Niimi
- Diabetic Neuropathy Project, Tokyo Metropolitan Institute of Medical Science, Setagaya, Tokyo 156-8506, Japan
| | - Koji Fukui
- Department of Bioscience and Engineering, Shibaura Institute of Technology, Saitama 337-8570, Japan
| | - Minoru Saitoe
- Learning and Memory Project, Tokyo Metropolitan Institute of Medical Science, Setagaya, Tokyo 156-8506, Japan
| | - Kazunori Sango
- Diabetic Neuropathy Project, Tokyo Metropolitan Institute of Medical Science, Setagaya, Tokyo 156-8506, Japan
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Li L, Diao S, Chen Z, Zhang J, Chen W, Wang T, Chen X, Zhao Y, Xu T, Huang C, Li J. DNMT3a-mediated methylation of TCF21/hnRNPA1 aggravates hepatic fibrosis by regulating the NF-κB signaling pathway. Pharmacol Res 2023; 193:106808. [PMID: 37268177 DOI: 10.1016/j.phrs.2023.106808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 05/28/2023] [Accepted: 05/28/2023] [Indexed: 06/04/2023]
Abstract
Hepatic fibrosis is caused by liver damage as a consequence of wound healing response. Recent studies have shown that hepatic fibrosis could be effectively reversed, partly through regression of activated hepatic stellate cells (HSCs). Transcription factor 21 (TCF21), a member of the basic helix-loop-helix (bHLH) transcription factor, is involved in epithelial-mesenchymal transformation in various diseases. However, the mechanism by which TCF21 regulates epithelial-mesenchymal transformation in hepatic fibrosis has not been elucidated. In this research, we found that hnRNPA1, the downstream binding protein of TCF21, accelerates hepatic fibrosis reversal by inhibiting the NF-κB signaling pathway. Furthermore, the combination of DNMT3a with TCF21 promoter results in TCF21 hypermethylation. Our results suggest that DNMT3a regulation of TCF21 is a significant event in reversing hepatic fibrosis. In conclusion, this research identifies a novel signaling axis, DNMT3a-TCF21-hnRNPA1, that regulates HSCs activation and hepatic fibrosis reversal, providing a novel treatment strategy for hepatic fibrosis. The clinical trial was registered in the Research Registry (researchregistry9079).
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Affiliation(s)
- Liangyun Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China; Institute for Liver Diseases of Anhui Medical University
| | - Shaoxi Diao
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China; Institute for Liver Diseases of Anhui Medical University
| | - Zixiang Chen
- The First Affiliated Hospital of Anhui Medical University, Hefei, 230032, China
| | - Jintong Zhang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China; Institute for Liver Diseases of Anhui Medical University
| | - Wei Chen
- The First Affiliated Hospital of Anhui Medical University, Hefei, 230032, China
| | - Tianqi Wang
- The First Affiliated Hospital of Anhui Medical University, Hefei, 230032, China
| | - Xin Chen
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China; Institute for Liver Diseases of Anhui Medical University
| | - Yuxin Zhao
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China; Institute for Liver Diseases of Anhui Medical University
| | - Tao Xu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China; Institute for Liver Diseases of Anhui Medical University
| | - Cheng Huang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China; Institute for Liver Diseases of Anhui Medical University.
| | - Jun Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China; Institute for Liver Diseases of Anhui Medical University.
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Panels of mRNAs and miRNAs for decoding molecular mechanisms of Renal Cell Carcinoma (RCC) subtypes utilizing Artificial Intelligence approaches. Sci Rep 2022; 12:16393. [PMID: 36180558 PMCID: PMC9525704 DOI: 10.1038/s41598-022-20783-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 09/19/2022] [Indexed: 11/12/2022] Open
Abstract
Renal Cell Carcinoma (RCC) encompasses three histological subtypes, including clear cell RCC (KIRC), papillary RCC (KIRP), and chromophobe RCC (KICH) each of which has different clinical courses, genetic/epigenetic drivers, and therapeutic responses. This study aimed to identify the significant mRNAs and microRNA panels involved in the pathogenesis of RCC subtypes. The mRNA and microRNA transcripts profile were obtained from The Cancer Genome Atlas (TCGA), which were included 611 ccRCC patients, 321 pRCC patients, and 89 chRCC patients for mRNA data and 616 patients in the ccRCC subtype, 326 patients in the pRCC subtype, and 91 patients in the chRCC for miRNA data, respectively. To identify mRNAs and miRNAs, feature selection based on filter and graph algorithms was applied. Then, a deep model was used to classify the subtypes of the RCC. Finally, an association rule mining algorithm was used to disclose features with significant roles to trigger molecular mechanisms to cause RCC subtypes. Panels of 77 mRNAs and 73 miRNAs could discriminate the KIRC, KIRP, and KICH subtypes from each other with 92% (F1-score ≥ 0.9, AUC ≥ 0.89) and 95% accuracy (F1-score ≥ 0.93, AUC ≥ 0.95), respectively. The Association Rule Mining analysis could identify miR-28 (repeat count = 2642) and CSN7A (repeat count = 5794) along with the miR-125a (repeat count = 2591) and NMD3 (repeat count = 2306) with the highest repeat counts, in the KIRC and KIRP rules, respectively. This study found new panels of mRNAs and miRNAs to distinguish among RCC subtypes, which were able to provide new insights into the underlying responsible mechanisms for the initiation and progression of KIRC and KIRP. The proposed mRNA and miRNA panels have a high potential to be as biomarkers of RCC subtypes and should be examined in future clinical studies.
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Liu D, Zhang Q, Luo P, Gu L, Shen S, Tang H, Zhang Y, Lyu M, Shi Q, Yang C, Wang J. Neuroprotective Effects of Celastrol in Neurodegenerative Diseases-Unscramble Its Major Mechanisms of Action and Targets. Aging Dis 2022; 13:815-836. [PMID: 35656110 PMCID: PMC9116906 DOI: 10.14336/ad.2021.1115] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 11/15/2021] [Indexed: 12/13/2022] Open
Abstract
There are rarely new therapeutic breakthroughs present for neurodegenerative diseases in the last decades. Thus, new effective drugs are urgently needed for millions of patients with neurodegenerative diseases. Celastrol, a pentacyclic triterpenoid compound, is one of the main active ingredients isolated from Tripterygium wilfordii Hook. f. that has multiple biological activities. Recently, amount evidence indicates that celastrol exerts neuroprotective effects and holds therapeutic potential to serve as a novel agent for neurodegenerative diseases. This review focuses on the therapeutic efficacy and major regulatory mechanisms of celastrol to rescue damaged neurons, restore normal cognitive and sensory motor functions in neurodegenerative diseases. Importantly, we highlight recent progress regarding identification of the drug targets of celastrol by using advanced quantitative chemical proteomics technology. Overall, this review provides novel insights into the pharmacological activities and therapeutic potential of celastrol for incurable neurodegenerative diseases.
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Affiliation(s)
- Dandan Liu
- 1Artemisinin research center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.,2Central People's Hospital of Zhanjiang, Zhanjiang, Guangdong, China
| | - Qian Zhang
- 1Artemisinin research center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.,2Central People's Hospital of Zhanjiang, Zhanjiang, Guangdong, China
| | - Piao Luo
- 1Artemisinin research center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.,2Central People's Hospital of Zhanjiang, Zhanjiang, Guangdong, China
| | - Liwei Gu
- 1Artemisinin research center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Shengnan Shen
- 1Artemisinin research center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Huan Tang
- 1Artemisinin research center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Ying Zhang
- 1Artemisinin research center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Ming Lyu
- 1Artemisinin research center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Qiaoli Shi
- 1Artemisinin research center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Chuanbin Yang
- 3Department of Geriatrics, Shenzhen People's Hospital, Shenzhen, China
| | - Jigang Wang
- 1Artemisinin research center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.,2Central People's Hospital of Zhanjiang, Zhanjiang, Guangdong, China.,3Department of Geriatrics, Shenzhen People's Hospital, Shenzhen, China.,4Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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9
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Timani KA, Rezaei S, Whitmill A, Liu Y, He JJ. Tip110/SART3-Mediated Regulation of NF-κB Activity by Targeting IκBα Stability Through USP15. Front Oncol 2022; 12:843157. [PMID: 35530338 PMCID: PMC9070983 DOI: 10.3389/fonc.2022.843157] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 03/21/2022] [Indexed: 11/25/2022] Open
Abstract
To date, there are a small number of nuclear-restricted proteins that have been reported to play a role in NF-κB signaling. However, the exact molecular mechanisms are not fully understood. Tip110 is a nuclear protein that has been implicated in multiple biological processes. In a previous study, we have shown that Tip110 interacts with oncogenic ubiquitin specific peptidase 15 (USP15) and that ectopic expression of Tip110 leads to re-distribution of USP15 from the cytoplasm to the nucleus. USP15 is known to regulate NF-κB activity through several mechanisms including modulation of IκBα ubiquitination. These findings prompted us to investigate the role of Tip110 in the NF-κB signaling pathway. We showed that Tip110 regulates NF-κB activity. The expression of Tip110 potentiated TNF-α-induced NF-κB activity and deletion of the nuclear localization domain in Tip110 abrogated this potentiation activity. We then demonstrated that Tip110 altered IκBα phosphorylation and stability in the presence of TNF-α. Moreover, we found that Tip110 and USP15 opposingly regulated NF-κB activity by targeting IκBα protein stability. We further showed that Tip110 altered the expression of NF-κB-dependent proinflammatory cytokines. Lastly, by using whole-transcriptome analysis of Tip110 knockout mouse embryonic stem cells, we found several NF-κB and NF-κB-related pathways were dysregulated. Taken together, these findings add to the nuclear regulation of NF-κB activity by Tip110 through IκBα stabilization and provide new evidence to support the role of Tip110 in controlling cellular processes such as cancers that involve proinflammatory responses.
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Affiliation(s)
- Khalid Amine Timani
- Department of Microbiology and Immunology, Rosalind Franklin University, Chicago Medical School, North Chicago, IL, United States
- Center for Cancer Cell Biology, Immunology and Infection, Rosalind Franklin University, North Chicago, IL, United States
- School of Graduate and Postdoctoral Studies, Rosalind Franklin University, North Chicago, IL, United States
- *Correspondence: Khalid Amine Timani,
| | - Sahar Rezaei
- Department of Microbiology and Immunology, Rosalind Franklin University, Chicago Medical School, North Chicago, IL, United States
- Center for Cancer Cell Biology, Immunology and Infection, Rosalind Franklin University, North Chicago, IL, United States
- School of Graduate and Postdoctoral Studies, Rosalind Franklin University, North Chicago, IL, United States
| | - Amanda Whitmill
- Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, United States
| | - Ying Liu
- Department of Microbiology and Immunology, Rosalind Franklin University, Chicago Medical School, North Chicago, IL, United States
- Center for Cancer Cell Biology, Immunology and Infection, Rosalind Franklin University, North Chicago, IL, United States
- School of Graduate and Postdoctoral Studies, Rosalind Franklin University, North Chicago, IL, United States
| | - Johnny J. He
- Department of Microbiology and Immunology, Rosalind Franklin University, Chicago Medical School, North Chicago, IL, United States
- Center for Cancer Cell Biology, Immunology and Infection, Rosalind Franklin University, North Chicago, IL, United States
- School of Graduate and Postdoctoral Studies, Rosalind Franklin University, North Chicago, IL, United States
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10
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Zhu C, Zhu Y, Zhang G, Wu H, Shi Y, Li J, Yang J, Mao Z, Xu Q, Yao X, Zhu X, Wang J, Liu X, Lin N. The analgesic and antidepressant properties of dihydroartemisinine in the neuropathic pain mice: By the downregulation of HnRNPA1 in the spinal cord and hippocampus. Clin Transl Med 2022; 12:e751. [PMID: 35220669 PMCID: PMC8882243 DOI: 10.1002/ctm2.751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/11/2022] [Accepted: 02/15/2022] [Indexed: 11/30/2022] Open
Affiliation(s)
- Chunyan Zhu
- Institute of Chinese Materia Medica China Academy of Chinese Medical Sciences Beijing China
| | - Yongping Zhu
- Artemisinin Research Center and Institute of Chinese Materia Medica China Academy of Chinese Medical Sciences Beijing China
| | - Guoxin Zhang
- Institute of Chinese Materia Medica China Academy of Chinese Medical Sciences Beijing China
| | - Hongyan Wu
- Institute of Chinese Materia Medica China Academy of Chinese Medical Sciences Beijing China
| | - Yuqi Shi
- Institute of Chinese Materia Medica China Academy of Chinese Medical Sciences Beijing China
| | - Jiahao Li
- Institute of Chinese Materia Medica China Academy of Chinese Medical Sciences Beijing China
| | - Jun Yang
- Institute of Chinese Materia Medica China Academy of Chinese Medical Sciences Beijing China
| | - Zhiyun Mao
- Institute of Chinese Materia Medica China Academy of Chinese Medical Sciences Beijing China
| | - Qionghong Xu
- Institute of Chinese Materia Medica China Academy of Chinese Medical Sciences Beijing China
| | - Xuemin Yao
- Institute of Chinese Materia Medica China Academy of Chinese Medical Sciences Beijing China
| | - Xiaoxin Zhu
- Institute of Chinese Materia Medica China Academy of Chinese Medical Sciences Beijing China
| | - Jigang Wang
- Artemisinin Research Center and Institute of Chinese Materia Medica China Academy of Chinese Medical Sciences Beijing China
| | - Xianguo Liu
- Department of Physiology and Pain Research Center Zhongshan School of Medicine Sun Yat‐sen University Guangzhou 510080 China
| | - Na Lin
- Institute of Chinese Materia Medica China Academy of Chinese Medical Sciences Beijing China
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11
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Pyne T, Ghosh P, Dhauria M, Ganguly K, Sengupta D, Nandagopal K, Sengupta M, Das M. Prioritization of human well-being spectrum related GWAS-SNVs using ENCODE-based web-tools predict interplay between PSMC3, ITIH4, and SERPINC1 genes in modulating well-being. J Psychiatr Res 2021; 145:92-101. [PMID: 34883412 DOI: 10.1016/j.jpsychires.2021.11.040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 04/16/2021] [Accepted: 11/21/2021] [Indexed: 11/23/2022]
Abstract
Several traits related to positive and negative affect show a high genetic as well as phenotypic correlation with well-being in humans, and are therefore collectively termed as "Well-being spectrum". Genome-Wide Association studies (GWA studies) on "well-being measurement" have led to identification of several genomic variants (Single Nucleotide Variants - SNVs), but very little has been explained with respect to their functionality and mode of alteration of well-being. Utilizing a pool of 1258 GWA studies based SNVs on "well-being measurement", we prioritized the SNVs and tried to annotate well-being related functionality through several bioinformatic tools to predict whether a protein sequence variation affects protein function, as well as experimentally validated datasets available in ENCODE based web-tools namely rSNPBase, RegulomeDB, Haploreg, along with GTEx Portal and STRING based protein interaction networks. Prioritization yielded three key SNVs; rs3781627-A, rs13072536-T and 5877-C potentially regulating three genes, PSMC3, ITIH4 and SERPINC1, respectively. Interestingly, the genes showed well clustered protein-protein interaction (maximum combined confidence score >0.4) with other well-being candidate genes, namely TNF and CRP genes suggesting their important role in modulation of well-being. PSMC3 and ITIH4 genes are also involved in driving acute phase responses signifying a probable cross-talk between well-being and psychoneuroimmunological system. To best of our knowledge this study is the first of its kind where the well-being associated GWA studies-SNVs were prioritized and functionally annotated, majorly based on functional data available in public domain, which revealed PSMC3, ITIH4 and SERPINC1 genes as probable candidates in regulation of well-being spectrum.
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Affiliation(s)
- Tushar Pyne
- Department of Genetics, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, India
| | - Poulomi Ghosh
- Department of Genetics, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, India
| | - Mrinmay Dhauria
- Department of Genetics, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, India
| | - Kausik Ganguly
- Department of Genetics, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, India
| | - Debmalya Sengupta
- Department of Genetics, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, India
| | - Krishnadas Nandagopal
- Department of Genetics, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, India
| | - Mainak Sengupta
- Department of Genetics, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, India.
| | - Madhusudan Das
- Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, West Bengal, 700019, India.
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12
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Knock-Down of Heterogeneous Nuclear Ribonucleoprotein A1 Results in Neurite Damage, Altered Stress Granule Biology, and Cellular Toxicity in Differentiated Neuronal Cells. eNeuro 2021; 8:ENEURO.0350-21.2021. [PMID: 34697074 PMCID: PMC8607908 DOI: 10.1523/eneuro.0350-21.2021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/29/2021] [Accepted: 10/18/2021] [Indexed: 12/13/2022] Open
Abstract
Heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) is an RNA binding protein (RBP) that is localized within neurons and plays crucial roles in RNA metabolism. Its importance in neuronal functioning is underscored from the study of its pathogenic features in many neurodegenerative diseases where neuronal hnRNP A1 is mislocalized from the nucleus to the cytoplasm resulting in loss of hnRNP A1 function. Here, we model hnRNP A1 loss-of-function by siRNA-mediated knock-down in differentiated Neuro-2a cells. Through RNA sequencing (RNA-seq) followed by gene ontology (GO) analyses, we show that hnRNP A1 is involved in important biological processes, including RNA metabolism, neuronal function, neuronal morphology, neuronal viability, and stress granule (SG) formation. We further confirmed several of these roles by showing that hnRNP A1 knock-down results in a reduction of neurite outgrowth, increase in cell cytotoxicity and changes in SG formation. In summary, these findings indicate that hnRNP A1 loss-of-function contributes to neuronal dysfunction and cell death and implicates hnRNP A1 dysfunction in the pathogenesis of neurodegenerative diseases.
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13
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Beijer D, Kim HJ, Guo L, O'Donovan K, Mademan I, Deconinck T, Van Schil K, Fare CM, Drake LE, Ford AF, Kochański A, Kabzińska D, Dubuisson N, Van den Bergh P, Voermans NC, Lemmers RJ, van der Maarel SM, Bonner D, Sampson JB, Wheeler MT, Mehrabyan A, Palmer S, De Jonghe P, Shorter J, Taylor JP, Baets J. Characterization of HNRNPA1 mutations defines diversity in pathogenic mechanisms and clinical presentation. JCI Insight 2021; 6:e148363. [PMID: 34291734 PMCID: PMC8410042 DOI: 10.1172/jci.insight.148363] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 06/03/2021] [Indexed: 12/13/2022] Open
Abstract
Mutations in HNRNPA1 encoding heterogeneous nuclear ribonucleoprotein (hnRNP) A1 are a rare cause of amyotrophic lateral sclerosis (ALS) and multisystem proteinopathy (MSP). hnRNPA1 is part of the group of RNA-binding proteins (RBPs) that assemble with RNA to form RNPs. hnRNPs are concentrated in the nucleus and function in pre-mRNA splicing, mRNA stability, and the regulation of transcription and translation. During stress, hnRNPs, mRNA, and other RBPs condense in the cytoplasm to form stress granules (SGs). SGs are implicated in the pathogenesis of (neuro-)degenerative diseases, including ALS and inclusion body myopathy (IBM). Mutations in RBPs that affect SG biology, including FUS, TDP-43, hnRNPA1, hnRNPA2B1, and TIA1, underlie ALS, IBM, and other neurodegenerative diseases. Here, we characterize 4 potentially novel HNRNPA1 mutations (yielding 3 protein variants: *321Eext*6, *321Qext*6, and G304Nfs*3) and 2 known HNRNPA1 mutations (P288A and D262V), previously connected to ALS and MSP, in a broad spectrum of patients with hereditary motor neuropathy, ALS, and myopathy. We establish that the mutations can have different effects on hnRNPA1 fibrillization, liquid-liquid phase separation, and SG dynamics. P288A accelerated fibrillization and decelerated SG disassembly, whereas *321Eext*6 had no effect on fibrillization but decelerated SG disassembly. By contrast, G304Nfs*3 decelerated fibrillization and impaired liquid phase separation. Our findings suggest different underlying pathomechanisms for HNRNPA1 mutations with a possible link to clinical phenotypes.
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Affiliation(s)
- Danique Beijer
- Translational Neurosciences, Faculty of Medicine and Health Sciences, and.,Laboratory for Neuromuscular Pathology, Institute Born-Bunge, University of Antwerp, Wilrijk, Belgium
| | - Hong Joo Kim
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Lin Guo
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Kevin O'Donovan
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Inès Mademan
- Translational Neurosciences, Faculty of Medicine and Health Sciences, and.,Laboratory for Neuromuscular Pathology, Institute Born-Bunge, University of Antwerp, Wilrijk, Belgium
| | - Tine Deconinck
- Medical Genetics, University of Antwerp and Antwerp University Hospital, Edegem, Belgium
| | - Kristof Van Schil
- Medical Genetics, University of Antwerp and Antwerp University Hospital, Edegem, Belgium
| | - Charlotte M Fare
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Lauren E Drake
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Alice F Ford
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Andrzej Kochański
- Neuromuscular Unit, Mossakowski Medical Research Centre, Polish Academy of Sciences, Warsaw, Poland
| | - Dagmara Kabzińska
- Neuromuscular Unit, Mossakowski Medical Research Centre, Polish Academy of Sciences, Warsaw, Poland
| | - Nicolas Dubuisson
- Neuromuscular Reference Centre, University Hospitals St-Luc, University of Louvain, Brussels, Belgium
| | - Peter Van den Bergh
- Neuromuscular Reference Centre, University Hospitals St-Luc, University of Louvain, Brussels, Belgium
| | - Nicol C Voermans
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | | | | | - Devon Bonner
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, California, USA
| | - Jacinda B Sampson
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, California, USA
| | - Matthew T Wheeler
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, California, USA
| | - Anahit Mehrabyan
- Department of Neurology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Steven Palmer
- Department of Neurology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Peter De Jonghe
- Translational Neurosciences, Faculty of Medicine and Health Sciences, and.,Laboratory for Neuromuscular Pathology, Institute Born-Bunge, University of Antwerp, Wilrijk, Belgium.,Neuromuscular Reference Centre, Department of Neurology, Antwerp University Hospital, Wilrijk, Belgium
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - J Paul Taylor
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Jonathan Baets
- Translational Neurosciences, Faculty of Medicine and Health Sciences, and.,Laboratory for Neuromuscular Pathology, Institute Born-Bunge, University of Antwerp, Wilrijk, Belgium.,Neuromuscular Reference Centre, Department of Neurology, Antwerp University Hospital, Wilrijk, Belgium
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14
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Wang Z, Li Y, Kuang X, Guo F, Lang T, Mao M, Zhang X, Yang H. Anti-proliferation and pro-apoptosis effects of miR-582-5p in chronic lymphocytic leukemia via targeting HNRNPA1 and suppression of NF-κB. Mol Cell Toxicol 2021. [DOI: 10.1007/s13273-021-00143-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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15
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Zhu C, Yang J, Zhu Y, Li J, Chi H, Tian C, Meng Y, Liu Y, Wang J, Lin N. Celastrol alleviates comorbid obesity and depression by directly binding amygdala HnRNPA1 in a mouse model. Clin Transl Med 2021; 11:e394. [PMID: 34185400 PMCID: PMC8181197 DOI: 10.1002/ctm2.394] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 04/03/2021] [Accepted: 04/07/2021] [Indexed: 11/24/2022] Open
Affiliation(s)
- Chunyan Zhu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jun Yang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yongping Zhu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jiahao Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Hongyu Chi
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Congmin Tian
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yuqing Meng
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yanqing Liu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jigang Wang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.,Shenzhen People's Hospital, Shenzhen, China.,Central People's Hospital of Zhanjiang, Zhanjiang, China
| | - Na Lin
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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16
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Ud Din Farooqee SB, Christie J, Venkatraman P. PSMD9 ribosomal protein network maintains nucleolar architecture and WT p53 levels. Biochem Biophys Res Commun 2021; 563:105-112. [PMID: 34077860 DOI: 10.1016/j.bbrc.2021.05.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 05/03/2021] [Indexed: 10/21/2022]
Abstract
Capitalizing on an unexpected observation that multiple free ribosomal proteins co-purify/pull-down with PSMD9, we report here for the first time that PSMD9 is necessary to maintain the morphology and integrity of the nucleolus. As seen by NPM1 immunofluorescence and electron microscopy, the nucleolar structure is clearly disrupted in PSMD9 null MCF7 breast cancer cells. The resultant stress is pronounced leading to the accumulation of WT p53 and slow growth. A dual insult with Actinomycin D exasperates the nucleolar stress in these cells which fail to recover in stipulated time. This double insult in the WT cells enhances the interaction of PSMD9 with ribosomal subunits. Our data also reveals that in PSMD9 null cells, ribosomal proteins RPS25 and RPL15 fail to localise in the nucleolus. We speculate that the interaction of PSMD9 with multiple free ribosome subunits has at least two important implications: a) PSMD9 plays a role in trafficking of ribosomal proteins into the nucleolus, therefore contributing to the maintenance of structural and morphological organization of the membrane-less nucleolar compartment; b) under conditions that induce nucleolar stress, PSMD9-Ribosomal Protein interaction protects WT MCF7 breast cancer cells from slow growth and eventual death. This possibility renders the domains of PSMD9 to be attractive drug targets in the context of cancer and other multiple ribosome-associated disorders.
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Affiliation(s)
- Sheikh Burhan Ud Din Farooqee
- Protein Interactome Lab for Structural and Functional Biology, Advanced Centre for Treatment, Research and Education in Cancer, Sector 22, Kharghar, Navi Mumbai, Maharashtra, 410210, India; Homi Bhabha National Institute, BARC Training School Complex, Anushaktinagar, Mumbai, Maharashtra, 400094, India
| | - Joel Christie
- Protein Interactome Lab for Structural and Functional Biology, Advanced Centre for Treatment, Research and Education in Cancer, Sector 22, Kharghar, Navi Mumbai, Maharashtra, 410210, India; Homi Bhabha National Institute, BARC Training School Complex, Anushaktinagar, Mumbai, Maharashtra, 400094, India
| | - Prasanna Venkatraman
- Protein Interactome Lab for Structural and Functional Biology, Advanced Centre for Treatment, Research and Education in Cancer, Sector 22, Kharghar, Navi Mumbai, Maharashtra, 410210, India; Homi Bhabha National Institute, BARC Training School Complex, Anushaktinagar, Mumbai, Maharashtra, 400094, India.
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17
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Structural Insights into Ankyrin Repeat-Containing Proteins and Their Influence in Ubiquitylation. Int J Mol Sci 2021; 22:ijms22020609. [PMID: 33435370 PMCID: PMC7826745 DOI: 10.3390/ijms22020609] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/05/2021] [Accepted: 01/07/2021] [Indexed: 12/12/2022] Open
Abstract
Ankyrin repeat (AR) domains are considered the most abundant repeat motif found in eukaryotic proteins. AR domains are predominantly known to mediate specific protein-protein interactions (PPIs) without necessarily recognizing specific primary sequences, nor requiring strict conformity within its own primary sequence. This promiscuity allows for one AR domain to recognize and bind to a variety of intracellular substrates, suggesting that AR-containing proteins may be involved in a wide array of functions. Many AR-containing proteins serve a critical role in biological processes including the ubiquitylation signaling pathway (USP). There is also strong evidence that AR-containing protein malfunction are associated with several neurological diseases and disorders. In this review, the structure and mechanism of key AR-containing proteins are discussed to suggest and/or identify how each protein utilizes their AR domains to support ubiquitylation and the cascading pathways that follow upon substrate modification.
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18
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Zheng W, Yan X, Huo R, Zhao X, Sun Y, Xu T. IRF11 enhances the inhibitory effect of IκBα on NF-κB activation in miiuy croaker. FISH & SHELLFISH IMMUNOLOGY 2020; 107:156-162. [PMID: 32961292 DOI: 10.1016/j.fsi.2020.09.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 09/06/2020] [Accepted: 09/07/2020] [Indexed: 06/11/2023]
Abstract
NF-κB is a typical transcription factor that regulates expression of various genes involved in inflammatory and immune responses. Therefore, it is essential that NF-κB signaling tightly regulated to maintain immune balance. Compared with those of mammals, the regulatory mechanisms of NF-κB signaling is rarely reported in teleost fish. IκBα is a prominent negative feedback regulator in the NF-κB signaling system. In this study, we determined that IRF11 enhances the inhibitory effect of IκBα on NF-κB activation in teleost fish. Overexpression of IRF11 can inhibit IκBα degradation, whereas its knockdown has the opposite effect of IκBα. Our study further indicates that IκBα was regulated via ubiquitin-proteasome degradation pathway, IRF11 inhibits IκBα in ubiquitin-proteasome degradation. This study provides a novel evidence on the regulation of innate immune signaling pathways in teleost fish and thus provides new insights into the regulatory mechanisms in mammals.
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Affiliation(s)
- Weiwei Zheng
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China; Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiaolong Yan
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China; Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Ruixuan Huo
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Xueyan Zhao
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Yuena Sun
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China; Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, 201306, China.
| | - Tianjun Xu
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China; Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, 201306, China; National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, 201306, China.
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19
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Zhao X, Yan X, Huo R, Xu T. IRF3 enhances NF-κB activation by targeting IκBα for degradation in teleost fish. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2020; 106:103632. [PMID: 31987876 DOI: 10.1016/j.dci.2020.103632] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/17/2020] [Accepted: 01/21/2020] [Indexed: 06/10/2023]
Abstract
Tightly regulation of NF-κB signaling is essential to innate and adaptive immune responses, but its regulatory mechanism remains unclear in various organisms, especially teleost fish. In this study, we reported that IRF3 attenuates the inhibitory effect of IκBα on NF-κB activation in teleost fish. Overexpression of IRF3 can promote IκBα degradation, whereas its knockdown can relieve degradation of IκBα. IRF3 promoted the degradation of IκBα protein, but this effect could be inhibited by MG132 treatment. IRF3 is crucial for the polyubiquitination and proteasomal degradation of IκBα. Our findings indicate that IRF3 regulates NF-κB pathway by targeting IκBα for ubiquitination and degradation. This study provides novel evidence on the regulation of innate immune signaling pathways in teleost fish and thus provides new insights into the regulatory mechanisms in mammals.
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Affiliation(s)
- Xueyan Zhao
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China; Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, 201306, China
| | - Xiaolong Yan
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China; Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, 201306, China
| | - Ruixuan Huo
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China; Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, 201306, China
| | - Tianjun Xu
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China; Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, 201306, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, 201306, China; International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, 201306, China.
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20
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Sahu I, Nanaware P, Mane M, Mulla SW, Roy S, Venkatraman P. Role of a 19S Proteasome Subunit- PSMD10 Gankyrin in Neurogenesis of Human Neural Progenitor Cells. Int J Stem Cells 2019; 12:463-473. [PMID: 31474027 PMCID: PMC6881037 DOI: 10.15283/ijsc19007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 06/21/2019] [Accepted: 08/06/2019] [Indexed: 12/13/2022] Open
Abstract
PSMD10Gankyrin, a proteasome assembly chaperone, is a widely known oncoprotein which aspects many hall mark properties of cancer. However, except proteasome assembly chaperon function its role in normal cell function remains unknown. To address this issue, we induced PSMD10Gankyrin overexpression in HEK293 cells and the resultant large-scale changes in gene expression profile were analyzed. We constituted networks from microarray data of these differentially expressed genes and carried out extensive topological analyses. The overrecurring yet consistent theme that appeared throughout analysis using varied network metrics is that all genes and interactions identified as important would be involved in neurogenesis and neuronal development. Intrigued we tested the possibility that PSMD10Gankyrin may be strongly associated with cell fate decisions that commit neural stem cells to differentiate into neurons. Overexpression of PSMD10Gankyrin in human neural progenitor cells facilitated neuronal differentiation via β-catenin Ngn1 pathway. Here for the first time we provide preliminary and yet compelling experimental evidence for the involvement of a potential oncoprotein – PSMD10Gankyrin, in neuronal differentiation.
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Affiliation(s)
- Indrajit Sahu
- Advance Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, India.,Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel.,Homi Bhabha National Institute, BARC Training School Complex, Mumbai, Maharashtra, India
| | - Padma Nanaware
- Advance Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, India.,Homi Bhabha National Institute, BARC Training School Complex, Mumbai, Maharashtra, India.,Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Minal Mane
- Advance Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, India
| | - Saim Wasi Mulla
- Advance Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, India.,Homi Bhabha National Institute, BARC Training School Complex, Mumbai, Maharashtra, India
| | - Soumen Roy
- Department of Physics, Bose Institute, Kolkata, India
| | - Prasanna Venkatraman
- Advance Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, India.,Homi Bhabha National Institute, BARC Training School Complex, Mumbai, Maharashtra, India
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21
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Postolache TT, del Bosque-Plata L, Jabbour S, Vergare M, Wu R, Gragnoli C. Co-shared genetics and possible risk gene pathway partially explain the comorbidity of schizophrenia, major depressive disorder, type 2 diabetes, and metabolic syndrome. Am J Med Genet B Neuropsychiatr Genet 2019; 180:186-203. [PMID: 30729689 PMCID: PMC6492942 DOI: 10.1002/ajmg.b.32712] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 11/16/2018] [Accepted: 12/07/2018] [Indexed: 12/20/2022]
Abstract
Schizophrenia (SCZ) and major depressive disorder (MDD) in treatment-naive patients are associated with increased risk for type 2 diabetes (T2D) and metabolic syndrome (MetS). SCZ, MDD, T2D, and MetS are often comorbid and their comorbidity increases cardiovascular risk: Some risk genes are likely co-shared by them. For instance, transcription factor 7-like 2 (TCF7L2) and proteasome 26S subunit, non-ATPase 9 (PSMD9) are two genes independently reported as contributing to T2D and SCZ, and PSMD9 to MDD as well. However, there are scarce data on the shared genetic risk among SCZ, MDD, T2D, and/or MetS. Here, we briefly describe T2D, MetS, SCZ, and MDD and their genetic architecture. Next, we report separately about the comorbidity of SCZ and MDD with T2D and MetS, and their respective genetic overlap. We propose a novel hypothesis that genes of the prolactin (PRL)-pathway may be implicated in the comorbidity of these disorders. The inherited predisposition of patients with SCZ and MDD to psychoneuroendocrine dysfunction may confer increased risk of T2D and MetS. We illustrate a strategy to identify risk variants in each disorder and in their comorbid psychoneuroendocrine and mental-metabolic dysfunctions, advocating for studies of genetically homogeneous and phenotype-rich families. The results will guide future studies of the shared predisposition and molecular genetics of new homogeneous endophenotypes of SCZ, MDD, and metabolic impairment.
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Affiliation(s)
- Teodor T. Postolache
- Department of Psychiatry, Mood and Anxiety Program, University of Maryland School of Medicine, Baltimore, Maryland,Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC), Veterans Integrated Service Network (VISN) 19, Military and Veteran Microbiome: Consortium for Research and Education (MVM-CoRE), Denver, Colorado,Mental Illness Research Education and Clinical Center (MIRECC), Veterans Integrated Service Network (VISN) 5, VA Capitol Health Care Network, Baltimore, Maryland
| | - Laura del Bosque-Plata
- National Institute of Genomic Medicine, Nutrigenetics and Nutrigenomic Laboratory, Mexico City, Mexico
| | - Serge Jabbour
- Department of Medicine, Division of Endocrinology, Diabetes, and Metabolic Disease, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Michael Vergare
- Department of Psychiatry and Human Behavior, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Rongling Wu
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, Pennsylvania,Department of Statistics, Penn State College of Medicine, Hershey, Pennsylvania
| | - Claudia Gragnoli
- Department of Medicine, Division of Endocrinology, Diabetes, and Metabolic Disease, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania,Department of Public Health Sciences, Penn State College of Medicine, Hershey, Pennsylvania,Molecular Biology Laboratory, Bios Biotech Multi-Diagnostic Health Center, Rome, Italy
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22
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Wang DW, Peng ZJ, Ren GF, Wang GX. The different roles of selective autophagic protein degradation in mammalian cells. Oncotarget 2016; 6:37098-116. [PMID: 26415220 PMCID: PMC4741918 DOI: 10.18632/oncotarget.5776] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 08/31/2015] [Indexed: 01/01/2023] Open
Abstract
Autophagy is an intracellular pathway for bulk protein degradation and the removal of damaged organelles by lysosomes. Autophagy was previously thought to be unselective; however, studies have increasingly confirmed that autophagy-mediated protein degradation is highly regulated. Abnormal autophagic protein degradation has been associated with multiple human diseases such as cancer, neurological disability and cardiovascular disease; therefore, further elucidation of protein degradation by autophagy may be beneficial for protein-based clinical therapies. Macroautophagy and chaperone-mediated autophagy (CMA) can both participate in selective protein degradation in mammalian cells, but the process is quite different in each case. Here, we summarize the various types of macroautophagy and CMA involved in determining protein degradation. For this summary, we divide the autophagic protein degradation pathways into four categories: the post-translational modification dependent and independent CMA pathways and the ubiquitin dependent and independent macroautophagy pathways, and describe how some non-canonical pathways and modifications such as phosphorylation, acetylation and arginylation can influence protein degradation by the autophagy lysosome system (ALS). Finally, we comment on why autophagy can serve as either diagnostics or therapeutic targets in different human diseases.
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Affiliation(s)
- Da-wei Wang
- Department of Biochemistry and Molecular Biology, School of Medicine, Shandong University, Jinan, Shandong, China
| | - Zhen-ju Peng
- Medical Institute of Paediatrics, Qilu Children's Hospital of Shandong University, Jinan, Shandong, China
| | - Guang-fang Ren
- Medical Institute of Paediatrics, Qilu Children's Hospital of Shandong University, Jinan, Shandong, China
| | - Guang-xin Wang
- Medical Institute of Paediatrics, Qilu Children's Hospital of Shandong University, Jinan, Shandong, China
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23
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Feng J, Li L, Tong L, Tang L, Wu S. The Involvement of Splicing Factor hnRNP A1 in UVB-induced Alternative Splicing of hdm2. Photochem Photobiol 2016; 92:318-324. [PMID: 26757361 DOI: 10.1111/php.12564] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 11/24/2015] [Indexed: 11/27/2022]
Abstract
Human homolog double minute 2 (hdm2), an oncoprotein, which binds to tumor suppressor p53 to facilitate its degradation, has been known to contribute to tumorigenesis. Its splicing variants are reported to be highly expressed in many cancers and can be induced by ultraviolet B light (UVB). However, the mechanisms of how UVB radiation induces hdm2 alternative splicing still remain unclear. In this study, we investigated the roles of two common splicing factors, heterogeneous nuclear ribonucleoproteins (hnRNP) A1 and serine/arginine-rich splicing factor 1 (SRSF1), in regulating UVB-induced hdm2 splicing. Our study indicated that while the expression of both hnRNP A1 and SRSF1 are induced, only hnRNP A1 is involved in hdm2 alternative splicing upon UVB irradiation. Overexpression of hnRNP A1 resulted in decrease of full-length hdm2 (hdm2-FL) and increase of hdm2B, one of hdm2 alternate-splicing forms; while down-regulated hnRNP A1 expression led to the decrease of the hdm2-FL and hdm2B in HaCaT cells. Protein-mRNA binding assay confirmed that UVB irradiation could increase the binding of hnRNP A1 to hdm2 pre-mRNA. In conclusion, we elucidated that UVB induces alternative splicing of hdm2 by increasing the expression and the binding of hnRNP A1 to hdm2 full-length mRNA.
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Affiliation(s)
- Jianguo Feng
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China.,Department of Chemistry and Biochemistry, Edison Biotechnology Institute, Ohio University, Athens, OH
| | - Li Li
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
| | - Lingying Tong
- Department of Chemistry and Biochemistry, Edison Biotechnology Institute, Ohio University, Athens, OH
| | - Liling Tang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
| | - Shiyong Wu
- Department of Chemistry and Biochemistry, Edison Biotechnology Institute, Ohio University, Athens, OH
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24
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Knockdown of HNRNPA1 inhibits lung adenocarcinoma cell proliferation through cell cycle arrest at G0/G1 phase. Gene 2016; 576:791-7. [DOI: 10.1016/j.gene.2015.11.009] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 11/08/2015] [Accepted: 11/09/2015] [Indexed: 01/21/2023]
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25
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Zhou B, Wang Y, Jiang J, Jiang H, Song J, Han T, Shi J, Qiao H. The long noncoding RNA colon cancer-associated transcript-1/miR-490 axis regulates gastric cancer cell migration by targeting hnRNPA1. IUBMB Life 2016; 68:201-10. [PMID: 26825578 DOI: 10.1002/iub.1474] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 12/30/2015] [Indexed: 01/17/2023]
Abstract
Colon cancer-associated transcript-1 (CCAT1) is a highly conserved long noncoding RNA that is deregulated in several cancers. However, its role in gastric carcinoma and its post-transcriptional regulation remain poorly understood. In this study, we provide the first evidence that CCAT1 regulates miR-490 in gastric cancer (GC) cells. Interestingly, miR-490 can also repress CCAT1 expression. CCAT1 expression was significantly upregulated, and miR-490 expression was downregulated in GC. The negative correlation between miR-490 and CCAT1 expression was observed in GC tissues. Importantly, CCAT1 contains a putative miR-490-binding site, and deletion of this binding site abolishes their miR-490 responsiveness. Post-transcriptional CCAT1 silencing by miR-490 significantly suppressed GC cell migration. Furthermore, miR-490 directly bound to the hnRNPA1 mRNA 3'-UTR to repress its translation. Inhibition of miR-490 rescued CCAT1 siRNA-mediated suppression of cell migration. hnRNPA1 expression was significantly upregulated in GC specimens, and there was a negative correlation between miR-490 and hnRNPA1 expression and also a positive correlation between hnRNAP1 expression level and CCAT1 level. Taken together, we show for the first time that the CCAT1/miR-490/hnRNPA1 axis promotes GC migration, and it may have a possible diagnostic and therapeutic potential in GC.
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Affiliation(s)
- Baoguo Zhou
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Yuli Wang
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Jinpeng Jiang
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Hongpeng Jiang
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Jianwei Song
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Taotao Han
- National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Juan Shi
- National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Haiquan Qiao
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
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26
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Hao H, Haas MJ, Wu R, Gragnoli C. T2D and Depression Risk Gene Proteasome Modulator 9 is Linked to Insomnia. Sci Rep 2015; 5:12032. [PMID: 26166263 PMCID: PMC4648424 DOI: 10.1038/srep12032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 06/15/2015] [Indexed: 12/18/2022] Open
Abstract
Insomnia increases type-2 diabetes (T2D) risk. The 12q24 locus is linked to T2D, depression, bipolar disorder and anxiety. At the 12q24 locus, the Proteasome-Modulator 9 (PSMD9) single nucleotide polymorphisms (SNPs) rs74421874 [intervening sequence (IVS) 3+nt460-G>A], rs3825172 (IVS3+nt437-C>T) and rs14259 (E197G-A>G) are linked to: T2D, depression, anxiety, maturity-onset-diabetes-of the young 3/MODY3, obesity, waist circumference, hypertension, hypercholesterolemia, T2D-macrovascular disease, T2D-microvascular disease, T2D-neuropathy, T2D-carpal-tunnel syndrome, T2D-nephropathy, T2D-retinopathy and non-diabetic retinopathy. PSMD9 SNP rs1043307/rs14259 (E197G-A>G) plays a role in anti-depressant therapy response, depression and schizophrenia. We aimed at determining PSMD9 rs74421874/rs3825172/rs14259 SNPs potential linkage to primary insomnia and sleep hours in T2D families. We recruited 200 Italian T2D families phenotyping them for primary insomnia and sleep hours per night. PSMD9-T2D-risk SNPs rs74421874/rs3825172 and rs1043307/rs14259 were tested for linkage with insomnia and sleep hours. Non-parametric-linkage analysis, linkage-disequilibrium-model analysis, single-SNP analysis, cluster-based-parametric analysis, quantitative-trait and variant-component analysis were performed using Merlin software. To validate data, 1000 replicates were executed for the significant non-parametric data. PSMD9 rs74421874 (IVS3+nt460-G>A), rs3825172 (IVS3+nt437-C>T) and rs1043307/rs14259 (E197G-A>G) SNPs are linked to insomnia in our Italian families.
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Affiliation(s)
- Han Hao
- Department of Statistics, Penn State University, State College, PA, USA
| | - Michael J. Haas
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Florida College of Medicine, Jacksonville, FL
| | - Rongling Wu
- Department of Statistics, Penn State University, State College, PA, USA
| | - Claudia Gragnoli
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Florida College of Medicine, Jacksonville, FL
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
- Center for Biotechnology and Department of Biology, Temple University’s College of Science & Technology, Philadelphia, PA, USA
- Molecular Biology Laboratory, Bios Biotech Multi-Diagnostic Health Center, Rome, Italy
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27
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L. Hopper J, Begum N, Smith L, A. Hughes T. The role of PSMD9 in human disease: future clinical and therapeutic implications. AIMS MOLECULAR SCIENCE 2015. [DOI: 10.3934/molsci.2015.4.476] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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28
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Sangith N, Srinivasaraghavan K, Sahu I, Desai A, Medipally S, Somavarappu AK, Verma C, Venkatraman P. Discovery of novel interacting partners of PSMD9, a proteasomal chaperone: Role of an Atypical and versatile PDZ-domain motif interaction and identification of putative functional modules. FEBS Open Bio 2014; 4:571-83. [PMID: 25009770 PMCID: PMC4087146 DOI: 10.1016/j.fob.2014.05.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 05/20/2014] [Accepted: 05/24/2014] [Indexed: 12/21/2022] Open
Abstract
The structure and functions of PSMD9, a proteasomal chaperone, are uncharacterized. PDZ-like domain of PSMD9 may recognize C-terminal residues in proteins. Using conserved C-terminal motifs in human proteome, we identify novel binding partners. hnRNPA1, GH, IL6-receptor, S14 and E12 interact with PSMD9 via a specific C-terminal motif. We predict and confirm residues in the PDZ domain that are involved in this interaction.
PSMD9 (Proteasome Macropain non-ATPase subunit 9), a proteasomal assembly chaperone, harbors an uncharacterized PDZ-like domain. Here we report the identification of five novel interacting partners of PSMD9 and provide the first glimpse at the structure of the PDZ-domain, including the molecular details of the interaction. We based our strategy on two propositions: (a) proteins with conserved C-termini may share common functions and (b) PDZ domains interact with C-terminal residues of proteins. Screening of C-terminal peptides followed by interactions using full-length recombinant proteins, we discovered hnRNPA1 (an RNA binding protein), S14 (a ribosomal protein), CSH1 (a growth hormone), E12 (a transcription factor) and IL6 receptor as novel PSMD9-interacting partners. Through multiple techniques and structural insights, we clearly demonstrate for the first time that human PDZ domain interacts with the predicted Short Linear Sequence Motif (SLIM) at the C-termini of the client proteins. These interactions are also recapitulated in mammalian cells. Together, these results are suggestive of the role of PSMD9 in transcriptional regulation, mRNA processing and editing, hormone and receptor activity and protein translation. Our proof-of-principle experiments endorse a novel and quick method for the identification of putative interacting partners of similar PDZ-domain proteins from the proteome and for discovering novel functions.
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Affiliation(s)
- Nikhil Sangith
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre (TMC), Kharghar, Navi Mumbai 410210, India
| | - Kannan Srinivasaraghavan
- Bioinformatics Institute ASTAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore ; Experimental Therapeutics Centre (A*STAR), 31 Biopolis Street, #03-01 Helios, Singapore 138669, Singapore
| | - Indrajit Sahu
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre (TMC), Kharghar, Navi Mumbai 410210, India
| | - Ankita Desai
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre (TMC), Kharghar, Navi Mumbai 410210, India
| | - Spandana Medipally
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre (TMC), Kharghar, Navi Mumbai 410210, India
| | - Arun Kumar Somavarappu
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre (TMC), Kharghar, Navi Mumbai 410210, India
| | - Chandra Verma
- Bioinformatics Institute ASTAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore ; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore ; Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
| | - Prasanna Venkatraman
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre (TMC), Kharghar, Navi Mumbai 410210, India
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